The 25 October coup in Sudan saw the military component of the transitional government assert itself over its civilian counterpart. In the weeks since, attention has mostly focused on events in Khartoum, but the coup, which was actively or tacitly supported by several of Sudan’s opposition groups, reveals much about how the military has successfully managed the political relationships with elites in the country’s conflict-affected peripheries and borderlands. In the first in a series of rapid response updates on the changing political and security situation in Sudan, we consider what impact recent events may have on the Juba Peace Agreement and, more generally, peace and security in Sudan’s conflict affected regions.